4da4 - Revision history

OCA at 10:43, 1 March 2024

2024-03-01T10:43:36Z

←Older revision		Revision as of 10:43, 1 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4da4]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DA4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DA4 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4da4]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DA4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DA4 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</scene>, <scene name='pdbligand=C49:4-THIO,5-FLUORO,5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>C49</scene>, <scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.6Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</scene>, <scene name='pdbligand=C49:4-THIO,5-FLUORO,5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>C49</scene>, <scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4da4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4da4 OCA], [https://pdbe.org/4da4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4da4 RCSB], [https://www.ebi.ac.uk/pdbsum/4da4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4da4 ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4da4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4da4 OCA], [https://pdbe.org/4da4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4da4 RCSB], [https://www.ebi.ac.uk/pdbsum/4da4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4da4 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/DNMT1_MOUSE DNMT1_MOUSE]] Methylates CpG residues. Preferentially methylates hemimethylated DNA. Associates with DNA replication sites in S phase maintaining the methylation pattern in the newly synthesized strand, that is essential for epigenetic inheritance. Associates with chromatin during G2 and M phases to maintain DNA methylation independently of replication. It is responsible for maintaining methylation patterns established in development. DNA methylation is coordinated with methylation of histones. Mediates transcriptional repression by direct binding to HDAC2. In association with DNMT3B and via the recruitment of CTCFL/BORIS, involved in activation of BAG1 gene expression by modulating dimethylation of promoter histone H3 at H3K4 and H3K9.<ref>PMID:11290321</ref> <ref>PMID:15550930</ref> <ref>PMID:17576694</ref>	+	[https://www.uniprot.org/uniprot/DNMT1_MOUSE DNMT1_MOUSE] Methylates CpG residues. Preferentially methylates hemimethylated DNA. Associates with DNA replication sites in S phase maintaining the methylation pattern in the newly synthesized strand, that is essential for epigenetic inheritance. Associates with chromatin during G2 and M phases to maintain DNA methylation independently of replication. It is responsible for maintaining methylation patterns established in development. DNA methylation is coordinated with methylation of histones. Mediates transcriptional repression by direct binding to HDAC2. In association with DNMT3B and via the recruitment of CTCFL/BORIS, involved in activation of BAG1 gene expression by modulating dimethylation of promoter histone H3 at H3K4 and H3K9.<ref>PMID:11290321</ref> <ref>PMID:15550930</ref> <ref>PMID:17576694</ref>
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	DNMT1, the major maintenance DNA methyltransferase in animals, helps to regulate gene expression, genome imprinting, and X-chromosome inactivation. We report on the crystal structure of a productive covalent mouse DNMT1(731-1602)-DNA complex containing a central hemimethylated CpG site. The methyl group of methylcytosine is positioned within a shallow hydrophobic concave surface, whereas the cytosine on the target strand is looped out and covalently anchored within the catalytic pocket. The DNA is distorted at the hemimethylated CpG step, with side chains from catalytic and recognition loops inserting through both grooves to fill an intercalation-type cavity associated with a dual base flip-out on partner strands. Structural and biochemical data establish how a combination of active and autoinhibitory mechanisms ensures the high fidelity of DNMT1-mediated maintenance DNA methylation.	+
-		+
-	Structure-based mechanistic insights into DNMT1-mediated maintenance DNA methylation.,Song J, Teplova M, Ishibe-Murakami S, Patel DJ Science. 2012 Feb 10;335(6069):709-12. PMID:22323818<ref>PMID:22323818</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 4da4" style="background-color:#fffaf0;"></div~~>	+

	==See Also==		==See Also==

OCA at 08:08, 21 September 2022

2022-09-21T08:08:36Z

←Older revision		Revision as of 08:08, 21 September 2022
Line 1:		Line 1:

	==Structure of mouse DNMT1 (731-1602) bound to hemimethylated CpG DNA==		==Structure of mouse DNMT1 (731-1602) bound to hemimethylated CpG DNA==
-	<StructureSection load='4da4' size='340' side='right' caption='[[4da4]], [[Resolution\|resolution]] 2.60Å' scene=''>	+	<StructureSection load='4da4' size='340' side='right'caption='[[4da4]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4da4]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Lk3_transgenic_mice Lk3 transgenic mice~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DA4 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4DA4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4da4]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DA4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DA4 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"~~><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</scene>, <scene name='pdbligand=C49:4-THIO,5-FLUORO,5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>C49</scene>, <scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	~~<tr~~ id~~='NonStdRes'><td class~~="~~sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat~~"><scene name='pdbligand=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</scene>, <scene name='pdbligand=C49:4-THIO,5-FLUORO,5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>C49</scene><~~/td></tr>~~	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4da4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4da4 OCA], [https://pdbe.org/4da4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4da4 RCSB], [https://www.ebi.ac.uk/pdbsum/4da4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4da4 ProSAT]</span></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">Dnmt1~~, ~~Dnmt, Met1, Uim ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice])~~<~~/td></tr>~~	+
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[http://en.wikipedia.org/wiki/DNA_(cytosine-5-)-methyltransferase DNA (cytosine-5-)-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.37 2.1.1.37]~~ </~~span~~></td></tr>	+
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4da4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4da4 OCA], [~~http~~://pdbe.org/4da4 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4da4 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4da4 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4da4 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/DNMT1_MOUSE DNMT1_MOUSE]] Methylates CpG residues. Preferentially methylates hemimethylated DNA. Associates with DNA replication sites in S phase maintaining the methylation pattern in the newly synthesized strand, that is essential for epigenetic inheritance. Associates with chromatin during G2 and M phases to maintain DNA methylation independently of replication. It is responsible for maintaining methylation patterns established in development. DNA methylation is coordinated with methylation of histones. Mediates transcriptional repression by direct binding to HDAC2. In association with DNMT3B and via the recruitment of CTCFL/BORIS, involved in activation of BAG1 gene expression by modulating dimethylation of promoter histone H3 at H3K4 and H3K9.<ref>PMID:11290321</ref> <ref>PMID:15550930</ref> <ref>PMID:17576694</ref>	+	[[https://www.uniprot.org/uniprot/DNMT1_MOUSE DNMT1_MOUSE]] Methylates CpG residues. Preferentially methylates hemimethylated DNA. Associates with DNA replication sites in S phase maintaining the methylation pattern in the newly synthesized strand, that is essential for epigenetic inheritance. Associates with chromatin during G2 and M phases to maintain DNA methylation independently of replication. It is responsible for maintaining methylation patterns established in development. DNA methylation is coordinated with methylation of histones. Mediates transcriptional repression by direct binding to HDAC2. In association with DNMT3B and via the recruitment of CTCFL/BORIS, involved in activation of BAG1 gene expression by modulating dimethylation of promoter histone H3 at H3K4 and H3K9.<ref>PMID:11290321</ref> <ref>PMID:15550930</ref> <ref>PMID:17576694</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 20:

	==See Also==		==See Also==
-	*[[DNA methyltransferase\|DNA methyltransferase]]	+	*[[DNA methyltransferase 3D structures\|DNA methyltransferase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Lk3 transgenic mice~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Patel, D J~~]]	+	[[Category: Mus musculus]]
-	[[Category: ~~Song, J~~]]	+	[[Category: Patel DJ]]
-	[[Category: ~~Covalent complex]]~~	+	[[Category: Song J]]
-	~~[[Category: Maintenance dna methylation]]~~	+
-	~~[[Category: Transferase-dna complex~~]]	+

OCA at 03:56, 5 August 2016

2016-08-05T03:56:00Z

←Older revision		Revision as of 03:56, 5 August 2016
Line 1:		Line 1:
		+
	==Structure of mouse DNMT1 (731-1602) bound to hemimethylated CpG DNA==		==Structure of mouse DNMT1 (731-1602) bound to hemimethylated CpG DNA==
	<StructureSection load='4da4' size='340' side='right' caption='[[4da4]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='4da4' size='340' side='right' caption='[[4da4]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4da4]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Mus_musculus Mus musculus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DA4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DA4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4da4]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DA4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DA4 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</scene>, <scene name='pdbligand=C49:4-THIO,5-FLUORO,5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>C49</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</scene>, <scene name='pdbligand=C49:4-THIO,5-FLUORO,5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>C49</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Dnmt1, Dnmt, Met1, Uim ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 ~~Mus musculus~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Dnmt1, Dnmt, Met1, Uim ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA_(cytosine-5-)-methyltransferase DNA (cytosine-5-)-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.37 2.1.1.37] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA_(cytosine-5-)-methyltransferase DNA (cytosine-5-)-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.37 2.1.1.37] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4da4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4da4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4da4 RCSB], [http://www.ebi.ac.uk/pdbsum/4da4 PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4da4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4da4 OCA], [http://pdbe.org/4da4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4da4 RCSB], [http://www.ebi.ac.uk/pdbsum/4da4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4da4 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 4da4" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 26:		Line 28:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Mus musculus~~]]	+	[[Category: Lk3 transgenic mice]]
	[[Category: Patel, D J]]		[[Category: Patel, D J]]
	[[Category: Song, J]]		[[Category: Song, J]]

OCA at 22:44, 24 December 2014

2014-12-24T22:44:21Z

←Older revision		Revision as of 22:44, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4da4]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DA4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DA4 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4da4]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DA4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DA4 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</scene>, <scene name='pdbligand=C49:4-THIO,5-FLUORO,5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>C49</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</scene>, <scene name='pdbligand=C49:4-THIO,5-FLUORO,5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>C49</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Dnmt1, Dnmt, Met1, Uim ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 Mus musculus])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Dnmt1, Dnmt, Met1, Uim ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 Mus musculus])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA_(cytosine-5-)-methyltransferase DNA (cytosine-5-)-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.37 2.1.1.37] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA_(cytosine-5-)-methyltransferase DNA (cytosine-5-)-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.37 2.1.1.37] </span></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4da4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4da4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4da4 RCSB], [http://www.ebi.ac.uk/pdbsum/4da4 PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4da4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4da4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4da4 RCSB], [http://www.ebi.ac.uk/pdbsum/4da4 PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DNMT1_MOUSE DNMT1_MOUSE]] Methylates CpG residues. Preferentially methylates hemimethylated DNA. Associates with DNA replication sites in S phase maintaining the methylation pattern in the newly synthesized strand, that is essential for epigenetic inheritance. Associates with chromatin during G2 and M phases to maintain DNA methylation independently of replication. It is responsible for maintaining methylation patterns established in development. DNA methylation is coordinated with methylation of histones. Mediates transcriptional repression by direct binding to HDAC2. In association with DNMT3B and via the recruitment of CTCFL/BORIS, involved in activation of BAG1 gene expression by modulating dimethylation of promoter histone H3 at H3K4 and H3K9.<ref>PMID:11290321</ref> <ref>PMID:15550930</ref> <ref>PMID:17576694</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 15:		Line 17:
	Structure-based mechanistic insights into DNMT1-mediated maintenance DNA methylation.,Song J, Teplova M, Ishibe-Murakami S, Patel DJ Science. 2012 Feb 10;335(6069):709-12. PMID:22323818<ref>PMID:22323818</ref>		Structure-based mechanistic insights into DNMT1-mediated maintenance DNA methylation.,Song J, Teplova M, Ishibe-Murakami S, Patel DJ Science. 2012 Feb 10;335(6069):709-12. PMID:22323818<ref>PMID:22323818</ref>

-	From ~~MEDLINEÂ®~~/~~PubMedÂ®~~, a database of the U.S. National Library of Medicine.<br>	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>

Line 25:		Line 27:
	</StructureSection>		</StructureSection>
	[[Category: Mus musculus]]		[[Category: Mus musculus]]
-	[[Category: Patel, D J.]]	+	[[Category: Patel, D J]]
-	[[Category: Song, J.]]	+	[[Category: Song, J]]
	[[Category: Covalent complex]]		[[Category: Covalent complex]]
	[[Category: Maintenance dna methylation]]		[[Category: Maintenance dna methylation]]
	[[Category: Transferase-dna complex]]		[[Category: Transferase-dna complex]]

OCA at 07:16, 5 June 2014

2014-06-05T07:16:08Z

←Older revision		Revision as of 07:16, 5 June 2014
Line 1:		Line 1:
-	[[~~Image:~~4da4.~~png~~\|~~left~~\|~~200px~~]]	+	==Structure of mouse DNMT1 (731-1602) bound to hemimethylated CpG DNA==
		+	<StructureSection load='4da4' size='340' side='right' caption='[[4da4]], [[Resolution\|resolution]] 2.60Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4da4]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DA4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DA4 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</scene>, <scene name='pdbligand=C49:4-THIO,5-FLUORO,5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>C49</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Dnmt1, Dnmt, Met1, Uim ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 Mus musculus])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA_(cytosine-5-)-methyltransferase DNA (cytosine-5-)-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.37 2.1.1.37] </span></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4da4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4da4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4da4 RCSB], [http://www.ebi.ac.uk/pdbsum/4da4 PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	DNMT1, the major maintenance DNA methyltransferase in animals, helps to regulate gene expression, genome imprinting, and X-chromosome inactivation. We report on the crystal structure of a productive covalent mouse DNMT1(731-1602)-DNA complex containing a central hemimethylated CpG site. The methyl group of methylcytosine is positioned within a shallow hydrophobic concave surface, whereas the cytosine on the target strand is looped out and covalently anchored within the catalytic pocket. The DNA is distorted at the hemimethylated CpG step, with side chains from catalytic and recognition loops inserting through both grooves to fill an intercalation-type cavity associated with a dual base flip-out on partner strands. Structural and biochemical data establish how a combination of active and autoinhibitory mechanisms ensures the high fidelity of DNMT1-mediated maintenance DNA methylation.

-	<!--	+	Structure-based mechanistic insights into DNMT1-mediated maintenance DNA methylation.,Song J, Teplova M, Ishibe-Murakami S, Patel DJ Science. 2012 Feb 10;335(6069):709-12. PMID:22323818<ref>PMID:22323818</ref>
-	~~The line below this paragraph~~, ~~containing "STRUCTURE_4da4"~~, ~~creates the "Structure Box" on the page~~.	+
-	~~You may change the PDB parameter~~ (~~which sets the PDB file loaded into the applet~~)	+
-	~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded),~~	+
-	~~or leave the SCENE parameter empty for the default display.~~	+
-	-->	+
-	~~{{STRUCTURE_4da4\| PDB=4da4 \| SCENE= }}~~	+

-	~~===Structure~~ of ~~mouse DNMT1 (731-1602) bound to hemimethylated CpG DNA===~~	+	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

-		+	==See Also==
-	~~<!--~~	+	*[[DNA methyltransferase\|DNA methyltransferase]]
-	~~The line below this paragraph, {{ABSTRACT_PUBMED_22323818}}, adds the Publication Abstract to the page~~	+	== References ==
-	~~(as it appears on PubMed at http://www.pubmed.gov), where 22323818 is the PubMed ID number.~~	+	<references/>
-	~~-->~~	+	__TOC__
-	~~{{ABSTRACT_PUBMED_22323818}}~~	+	</StructureSection>
-		+
-	==~~About this Structure~~==	+
-	[[~~4da4~~]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DA4 OCA].	+
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:022323818<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Mus musculus]]		[[Category: Mus musculus]]
	[[Category: Patel, D J.]]		[[Category: Patel, D J.]]

OCA at 08:44, 29 February 2012

2012-02-29T08:44:17Z

←Older revision		Revision as of 08:44, 29 February 2012
Line 1:		Line 1:
-	[[Image:4da4.~~jpg~~\|left\|200px]]	+	[[Image:4da4.png\|left\|200px]]

	<!--		<!--
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	===Structure of mouse DNMT1 (731-1602) bound to hemimethylated CpG DNA===		===Structure of mouse DNMT1 (731-1602) bound to hemimethylated CpG DNA===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_22323818}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 22323818 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_22323818}}

	==About this Structure==		==About this Structure==

OCA at 07:46, 22 February 2012

2012-02-22T07:46:47Z

←Older revision		Revision as of 07:46, 22 February 2012
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:4da4.jpg\|left\|200px]]

-	The ~~entry 4da4~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_4da4", creates the "Structure Box" on the page.
		+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
		+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
		+	or leave the SCENE parameter empty for the default display.
		+	-->
		+	{{STRUCTURE_4da4\| PDB=4da4 \| SCENE= }}

-	~~Authors: Song, J., Patel, D.J.~~	+	===Structure of mouse DNMT1 (731-1602) bound to hemimethylated CpG DNA===

-	~~Description:~~ Structure ~~of mouse DNMT1 (731~~-~~1602) bound to hemimethylated CpG DNA~~	+
		+	==About this Structure==
		+	[[4da4]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DA4 OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:022323818</ref><references group="xtra"/>
		+	[[Category: Mus musculus]]
		+	[[Category: Patel, D J.]]
		+	[[Category: Song, J.]]
		+	[[Category: Covalent complex]]
		+	[[Category: Maintenance dna methylation]]
		+	[[Category: Transferase-dna complex]]

OCA at 06:09, 25 January 2012

2012-01-25T06:09:23Z

←Older revision		Revision as of 06:09, 25 January 2012
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4da4 is ON HOLD	+	The entry 4da4 is ON HOLD until Paper Publication

	Authors: Song, J., Patel, D.J.		Authors: Song, J., Patel, D.J.

	Description: Structure of mouse DNMT1 (731-1602) bound to hemimethylated CpG DNA		Description: Structure of mouse DNMT1 (731-1602) bound to hemimethylated CpG DNA

OCA: Protected "4da4" [edit=sysop:move=sysop]

2012-01-18T10:28:22Z

Protected "4da4" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:28, 18 January 2012

OCA: New page: '''Unreleased structure''' The entry 4da4 is ON HOLD Authors: Song, J., Patel, D.J. Description: Structure of mouse DNMT1 (731-1602) bound to hemimethylated CpG DNA

2012-01-18T10:28:21Z

New page: '''Unreleased structure''' The entry 4da4 is ON HOLD Authors: Song, J., Patel, D.J. Description: Structure of mouse DNMT1 (731-1602) bound to hemimethylated CpG DNA

New page

'''Unreleased structure'''

The entry 4da4 is ON HOLD

Authors: Song, J., Patel, D.J.

Description: Structure of mouse DNMT1 (731-1602) bound to hemimethylated CpG DNA